plotSpatialAnnotations: Plot spatial annotations

In theMILOlab/SPATA2: A Toolbox for Spatial Expression Analysis

Plot spatial annotations

Description

Plots image sections containing the areas that were annotated via createGroupAnnotations(), createImageAnnotations() or createNumericAnnotations() .

Usage

plotSpatialAnnotations(object, ...)

## S4 method for signature 'SPATA2'
plotSpatialAnnotations(
  object,
  ids = NULL,
  tags = NULL,
  test = "any",
  expand = "25%",
  square = TRUE,
  outline = TRUE,
  inner = TRUE,
  unit = getSpatialMethod(object)@unit,
  round = 2,
  line_color = "black",
  line_size = 1.5,
  line_type = "solid",
  fill = "orange",
  alpha = 0.25,
  sb_dist = FALSE,
  display_title = FALSE,
  display_subtitle = TRUE,
  display_caption = FALSE,
  ggpLayers = list(),
  nrow = NULL,
  ncol = NULL,
  plot = TRUE,
  ...
)

## S4 method for signature 'SpatialData'
plotSpatialAnnotations(
  object,
  ids = NULL,
  tags = NULL,
  test = "any",
  expand = "25%",
  square = TRUE,
  outline = TRUE,
  inner = TRUE,
  unit = getSpatialMethod(object)@unit,
  round = 2,
  line_color = "black",
  line_size = 1.5,
  line_type = "solid",
  fill = "orange",
  alpha = 0.25,
  sb_dist = FALSE,
  display_title = FALSE,
  display_subtitle = TRUE,
  display_caption = FALSE,
  ggpLayers = list(),
  nrow = NULL,
  ncol = NULL,
  plot = TRUE,
  ...
)

Arguments

object	An object of class SPATA2 or, in case of S4 generics, objects of classes for which a method has been defined.
...	Additional arguments given to ggpLayerScaleBarSI() if input for sb_dist is a valid distance measure. Exception: xrange and yrange are set to the ranges of the image that was cropped to display the spatial annotation.
tags	Character vector or NULL. If character, the tags for the image annotation selection. See section Selection of spatial annotations for more information.
test	Character value. One of c('any'. 'all', 'identical', 'not_identical', 'none'). Specifies how input for tags is used to select spatial annotations. See section Selection of spatial annotations for more information.
expand	Specifies image expansion. An image that is cropped based on an image annotation centers around the image annotation. If expand = 0, the default, the dimensions of the image, that is width/x-axis and height/y-axis, are set to include only the image annotation area and nothing more. Using expand, the cropped image section can be adjusted. See section Expansion of cropped image sections for more information.
square	Logical value. Most image annotations come in variable shapes and have different horizontal and vertical diameters. Therefore, height and width of the image section are usually not equal. If square = TRUE, the cropped section of the image that contains the annotated structure is forced into a square: the bigger diameter of both is taken as default. E.g. if the horizontal diameter of the image annotation is 1mm and the vertical diameter is 1.5mm, the output image will have height and width of 1.5mm. That is, in terms of coordinates, an x-range and a y-range of 1.5mm. Processing of the image output depending on argument expand happens afterwards.
outline	Logical value. If TRUE, a polygon is drawn around the exact extent of the annotated structure.
inner	Logical value. Only applies if an image annotation contains a secondary image annotation within its own area. If FALSE, the inner borders of the image annotation are not included in the output.
unit	Character value. The unit in which the x- and y-axis text are displayed. Use validUnitsOfLengthSI() to obtain all valid input options.
round	Numeric value or FALSE. If numeric and unit is not px, rounds axes text.
line_color	Character. Affects color of the main lines of the plot.
line_size	Numeric. Affects size of the main lines of the plot.
line_type	Character. The line type. One of 'blank', 'solid', 'dashed', 'dotted', 'dotdash', 'longdash' and 'twodash'.
fill	Character value or NA. If character, specifies the color with which the outline of the spatial annotation is filled.
sb_dist	Distance measure or FALSE. If distance measure, defines the distance in SI units that a scale bar illustrates. Scale bar is plotted with ggpLayerScaleBarSI(). If FALSE, no scale bar is plotted.
display_title	Logical value. If TRUE, the number of each spatial annotation is plotted in the title.
display_subtitle	Logical value. If TRUE, the ID of each spatial annotation is plotted in the subtitle.
display_caption	Logial value. If TRUE, the tags of each spatial annotation are plotted in the caption.
ggpLayers	List of ggproto-objects that are added to each plot. Skim ggpLayer*()-functions for more options.
nrow, ncol	Numeric values or NULL. Used to arrange multiple plots.
plot	Logical value. If TRUE, the plots are plotted immediately via gridExtra.grid.arrange() and the list of plots is returned invisibly. Else the list of plots is simply returned.

Details

At first, the image section that contains the spatial annotation is cropped such that it only contains the extent of the polygon that represents the borders of the annotation (ranges can be obtained with getSpatAnnRange()). Using arguments square and expand can be used to expand the displayed image section individually.

Value

A list of ggplots. Each slot contains a plot that visualizes an spatial annotation.

Distance measures

The vignette on distance measures in SPATA2 has been replaced. Click here to read it.

Expansion of cropped image sections

The argument expand is a versatile way, to specify how a cropped image section is extracted. If you want the cropped image as is, specify expand = 0. Else, there are multiple options. In general, expand takes three kinds of values, namely percentages, distances and distance exclamations.

• Percentage: A string suffixed with %. E.g. expand = '50%' adds 50% of the distance from the center to the border of the image annotation to the image frame.

• Distance measures: In pixel or European units of length. E.g. expand = list(x = '1mm') expands the x-axis on both sides with 1mm. ⁠expand = list(x = c('0.5mm', 1.5mm')⁠ expands the x-axis on the left side with 0.5mm and on the right side with 1.5mm.

• Exclam distance measures: Distance measure with an exclamation mark suffix. E.g. expand = '1mm!' centers the image and forces an axis length of 1 millimeter. (Example 5)

Depending on how the values are specified different parts of the image can be expanded.

Single values, like expand = 50, are recycled: Every end of each image axis is expanded by 50 pixel. (Example 2)

Vectors of length two, like expand = c('1mm', '2mm'), are recycled: The beginning of each axis is expanded by 1 millimeter. The end of each axis is expanded by 2mm. (Example 3)

Named lists can be more precise. expand = list(x = c('1mm', '0.5mm'), y = c('0.25mm', '1mm')). Applies the vectors to expand the corresponding axis. (Example 4)

Using exclam input the side of the axis must not be specified as the axis is fixed as a whole. E.g expand = list(x = '1mm!', y = '2mm!') results in the same output as ⁠expand = list(x = c('1mm!', '1mm!'), y = c('2mm!', '2mm!')⁠.

Selection of spatial annotations

Selection of spatial annotations via the arguments ids, class, tags and test works in three steps:

First, if ids is a character it prefilters the annotations by ID and only the specified ones are submitted to the next steps. If it is NULL, all annotations are submitted to the next steps.

Secondd, if class is a character it filters the annotations remaining after the first step by their class. If NULL, the step is skipped.

Third, if tags is a character it is used in combination with test to select from the spatial annotations that remain after the second step based on the meta data they are tagged with. There are multiple options:

1. Argument test set to 'any' or 1: To be included, an image annotation must be tagged with at least one of the input tags.

2. Argument test set to 'all' or 2: To be included, an image annotation must be tagged with all of the input tags. Can contain tags that are not specified.

3. Argument test set to 'identical' or 3: To be included, an image annotation must be tagged with all of the input tags. Can not be tagged with anything else.

4. Argument test set to not_identical or 4: To be included, an image annotation must not be tagged with the combination of input tags.

5. Argument test set to 'none' or 5: To be included, an image annotation must not contain any of the input tags.

If tags is NULL, the step is skipped. Therefore, if ids, class and tags are all NULL, which is the default, all annotations are selected as all subsetting steps are skipped. Eventually, the remaining spatial annotations are submitted to whatever the respective function does.

See Also

getSpatialAnnotations()

Examples

library(SPATA2)

data("example_data")

object <- example_data$object_UKF313T_diet

ids <- getSpatAnnIds(object, tags = c("necrotic", "compr"), test = "identical")

plotSpatialAnnotations(object, ids = ids)

plotSpatialAnnotations(object, ids = ids, square = T)

plotSpatialAnnotations(object, id = ids, fill = "orange", square = T, expand = "50%")

theMILOlab/SPATA2 documentation built on Feb. 8, 2025, 11:41 p.m.